Navalny had accused the FSB of poisoning him during his visit to the Siberian city of Tomsk in August 2020.
The 235th military court in Moscow on Monday threw the complaint out over a lack of sound evidence.
The court ruled that it was lawful for the federal investigators to refuse to look into the matter formally, a decision they said was justified by ‘a lack of evidence’ that a crime had taken place.
Navalny accuses Russian investigators of not launching criminal proceedings to find the evidence for the alleged poisoning attack.
Back in August, Siberian police had conducted preliminary checks after Navalny was hospitalized, but refused to launch a criminal investigation into the case citing the ‘lack of the event of a crime.’
Navalny claims the poisoning was carried out on the direct order of President Vladimir Putin.
The Western-backed opposition figure is serving a two-and-a-half year sentence in a penal colony east of Moscow.
During his visit to Tomsk, Navalny fell violently ill on his flight over Siberia. Within days, he was airlifted to Germany for medical treatment. He spent months in recovery there.
Western sources claimed Navalny had been poisoned with Novichok agent, a Soviet-designed nerve toxin.
After returning to Moscow in mid-January, Navalny was immediately detained by authorities on charges of violating parole while abroad and in February he was sentenced to jail time.
The Kremlin, which has denied any involvement with Navalny illness, has accused German authorities of refusing to cooperate on the Russian investigation.